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Lig3 DNA ligase 3 [ Rattus norvegicus (Norway rat) ]

Gene ID: 303369, updated on 2-Nov-2024

Summary

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Official Symbol
Lig3provided by RGD
Official Full Name
DNA ligase 3provided by RGD
Primary source
RGD:1309875
See related
EnsemblRapid:ENSRNOG00000021815 AllianceGenome:RGD:1309875
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Enables DNA ligase activity. Involved in base-excision repair, DNA ligation. Predicted to be located in mitochondrion; nucleoplasm; and synaptonemal complex. Predicted to be part of DNA ligase III-XRCC1 complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in mitochondrial DNA depletion syndrome 20 and pancreatic cancer. Orthologous to human LIG3 (DNA ligase 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Testes (RPKM 146.4), Thymus (RPKM 143.6) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Lig3 in Genome Data Viewer
Location:
10q26
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (68215371..68238705)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (67717808..67741141)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (70134734..70158051)

Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene chaperonin containing TCP1 subunit 6B Neighboring gene zinc finger protein 830 Neighboring gene uncharacterized LOC102547954 Neighboring gene ring finger and FYVE-like domain containing E3 ubiquitin protein ligase Neighboring gene RAD51 paralog D Neighboring gene U6 spliceosomal RNA Neighboring gene fibronectin type III domain containing 8

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Involvement of DNA ligase III and ribonuclease H1 in mitochondrial DNA replication in cultured human cells. Ruhanen H, et al. Biochim Biophys Acta, 2011 Dec. PMID 21878356, Free PMC Article
  2. Mammalian DNA ligase III: molecular cloning, chromosomal localization, and expression in spermatocytes undergoing meiotic recombination. Chen J, et al. Mol Cell Biol, 1995 Oct. PMID 7565692, Free PMC Article
  3. The human DNA ligase III gene encodes nuclear and mitochondrial proteins. Lakshmipathy U, et al. Mol Cell Biol, 1999 May. PMID 10207110, Free PMC Article
  4. Early embryonic lethality due to targeted inactivation of DNA ligase III. Puebla-Osorio N, et al. Mol Cell Biol, 2006 May. PMID 16648486, Free PMC Article
  5. CircRNA Galntl6 sponges miR-335 to ameliorate stress-induced hypertension through upregulating Lig3 in rostral ventrolateral medulla. Zhang S, et al. Redox Biol, 2023 Aug. PMID 37315345, Free PMC Article

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CircRNA Galntl6 sponges miR-335 to ameliorate stress-induced hypertension through upregulating Lig3 in rostral ventrolateral medulla.
    Title: CircRNA Galntl6 sponges miR-335 to ameliorate stress-induced hypertension through upregulating Lig3 in rostral ventrolateral medulla.
Submit: New GeneRIF Correction

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA ligase (ATP) activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA ligase (ATP) activity ISO
Inferred from Sequence Orthology
more info
  
enables DNA ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA ligase activity ISO
Inferred from Sequence Orthology
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in DNA biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA ligation ISO
Inferred from Sequence Orthology
more info
  
NOT involved_in V(D)J recombination ISO
Inferred from Sequence Orthology
more info
  
involved_in base-excision repair, DNA ligation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in base-excision repair, DNA ligation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in base-excision repair, DNA ligation ISO
Inferred from Sequence Orthology
more info
  
involved_in double-strand break repair IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in double-strand break repair ISO
Inferred from Sequence Orthology
more info
  
involved_in double-strand break repair via alternative nonhomologous end joining ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within double-strand break repair via nonhomologous end joining ISO
Inferred from Sequence Orthology
more info
  
involved_in lagging strand elongation IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within mitochondrial DNA repair ISO
Inferred from Sequence Orthology
more info
  
involved_in mitochondrial DNA repair ISO
Inferred from Sequence Orthology
more info
  
involved_in mitochondrion organization ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within negative regulation of DNA recombination ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of mitochondrial DNA replication ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of DNA ligase III-XRCC1 complex ISO
Inferred from Sequence Orthology
more info
  
located_in condensed nuclear chromosome ISO
Inferred from Sequence Orthology
more info
  
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrion ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in synaptonemal complex ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
DNA ligase 3
Names
DNA ligase (ATP) 3
ligase III, DNA, ATP-dependent
NP_001380964.1
NP_001380965.1
XP_008766242.2
XP_008766243.2
XP_038941956.1
XP_038941957.1
XP_038941958.1
XP_038941959.2
XP_063125149.1
XP_063125150.1
XP_063125151.1
XP_063125152.1
XP_063125153.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001394035.1 → NP_001380964.1  DNA ligase 3 isoform 1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000010
    UniProtKB/TrEMBL
    A0A0G2JV76, A6HHE1
    Conserved Domains (3) summary
    TIGR00574
    Location:320 → 832
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97 → 182
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:927 → 997
    LIG3_BRCT; DNA ligase 3 BRCT domain

  2. NM_001394036.1 → NP_001380965.1  DNA ligase 3 isoform 1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000010
    UniProtKB/TrEMBL
    A0A0G2JV76, A6HHE1
    Related
    ENSRNOP00000068489.3, ENSRNOT00000076739.4
    Conserved Domains (3) summary
    TIGR00574
    Location:320 → 832
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97 → 182
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:927 → 997
    LIG3_BRCT; DNA ligase 3 BRCT domain

RNA

  1. NR_172067.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000010

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086028.1 Reference GRCr8

    Range
    68215371..68238705
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039086031.2 → XP_038941959.2  DNA ligase 3 isoform X8

  2. XM_008768020.4 → XP_008766242.2  DNA ligase 3 isoform X2

  3. XM_063269083.1 → XP_063125153.1  DNA ligase 3 isoform X7

    Related
    ENSRNOP00000069379.3, ENSRNOT00000084076.3

  4. XM_063269081.1 → XP_063125151.1  DNA ligase 3 isoform X5

    Related
    ENSRNOP00000052836.3, ENSRNOT00000055982.6

  5. XM_008768021.4 → XP_008766243.2  DNA ligase 3 isoform X4

  6. XM_063269079.1 → XP_063125149.1  DNA ligase 3 isoform X1

  7. XM_039086029.2 → XP_038941957.1  DNA ligase 3 isoform X3

    UniProtKB/TrEMBL
    A0A0G2JV76, A6HHE1
    Conserved Domains (3) summary
    TIGR00574
    Location:320 → 832
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97 → 182
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:927 → 997
    LIG3_BRCT; DNA ligase 3 BRCT domain

  8. XM_039086030.2 → XP_038941958.1  DNA ligase 3 isoform X3

    UniProtKB/TrEMBL
    A0A0G2JV76, A6HHE1
    Conserved Domains (3) summary
    TIGR00574
    Location:320 → 832
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97 → 182
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:927 → 997
    LIG3_BRCT; DNA ligase 3 BRCT domain

  9. XM_063269080.1 → XP_063125150.1  DNA ligase 3 isoform X3

  10. XM_039086028.2 → XP_038941956.1  DNA ligase 3 isoform X3

    UniProtKB/TrEMBL
    A0A0G2JV76, A6HHE1
    Conserved Domains (3) summary
    TIGR00574
    Location:320 → 832
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97 → 182
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:927 → 997
    LIG3_BRCT; DNA ligase 3 BRCT domain

  11. XM_063269082.1 → XP_063125152.1  DNA ligase 3 isoform X6

Nucleotide Protein Strain
Heading Accession and Version

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